LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# Simple rigid body system

units		lj
atom_style	atomic

pair_style	lj/cut 2.5

read_data	data.rigid
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  81 atoms

velocity 	all create 100.0 4928459

# unconnected bodies

#group		clump1 id <> 1 9
#group		clump2 id <> 10 18
#group		clump3 id <> 19 27
#group		clump4 id <> 28 36
#group		clump5 id <> 37 45
#group		clump6 id <> 46 54
#group		clump7 id <> 55 63
#group		clump8 id <> 64 72
#group		clump9 id <> 73 81

#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 #	  	      clump6 clump7 clump8 clump9

# 1 chain of connected bodies

group		clump1 id <> 1 9
9 atoms in group clump1
group		clump2 id <> 9 18
10 atoms in group clump2
group		clump3 id <> 18 27
10 atoms in group clump3
group		clump4 id <> 27 36
10 atoms in group clump4
group		clump5 id <> 36 45
10 atoms in group clump5
group		clump6 id <> 45 54
10 atoms in group clump6
group		clump7 id <> 54 63
10 atoms in group clump7
group		clump8 id <> 63 72
10 atoms in group clump8
group		clump9 id <> 72 81
10 atoms in group clump9

fix 1 all poems group clump1 clump2 clump3 clump4 clump5 	  	      clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms

# 2 chains of connected bodies

#group		clump1 id <> 1 9
#group		clump2 id <> 9 18
#group		clump3 id <> 18 27
#group		clump4 id <> 27 36
#group		clump5 id <> 37 45
#group		clump6 id <> 45 54
#group		clump7 id <> 54 63
#group		clump8 id <> 63 72
#group		clump9 id <> 72 81

#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9

neigh_modify	exclude group clump1 clump1
neigh_modify	exclude group clump2 clump2
neigh_modify	exclude group clump3 clump3
neigh_modify	exclude group clump4 clump4
neigh_modify	exclude group clump5 clump5
neigh_modify	exclude group clump6 clump6
neigh_modify	exclude group clump7 clump7
neigh_modify	exclude group clump8 clump8
neigh_modify	exclude group clump9 clump9

thermo		100

#dump		1 all atom 50 dump.rigid.poems

#dump		2 all image 100 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30
#dump_modify	2 pad 5

#dump		3 all movie 100 movie.mpg type type #		axes yes 0.8 0.02 view 60 -30
#dump_modify	3 pad 5

timestep 	0.0001
thermo		50
run		10000
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 18 18 18
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.263 | 3.357 | 3.638 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0     217.7783    3430.3907            0    3466.6871   -2.7403788 
      50    13679.637    1404.2468            0    3684.1863    12.446066 
     100    16777.225    888.87665            0    3685.0808   -31.828677 
     150    19595.365    418.45042            0    3684.3446    40.709078 
     200    18524.188    596.47273            0    3683.8375   -0.8159371 
     250    21015.789    180.96521            0    3683.5967   -10.042469 
     300    20785.513    219.25314            0    3683.5053    2.6452719 
     350     21072.46     171.2554            0    3683.3321    7.0609024 
     400    19956.414    356.36381            0    3682.4328    19.320259 
     450     20724.42    227.73284            0    3681.8028    8.1259249 
     500    20152.578    322.71466            0    3681.4777    5.4929878 
     550    20017.022    345.29701            0    3681.4673    5.4661666 
     600    17897.743    698.72196            0    3681.6791    3.2854742 
     650    17297.758    796.60256            0    3679.5623    15.191113 
     700    18581.934    584.29715            0    3681.2861    5.1588289 
     750    21774.158    52.821062            0    3681.8474   -10.775664 
     800    21604.055    81.188546            0    3681.8644   -3.2045743 
     850    17821.483    711.53827            0    3681.7854    7.4384276 
     900    21033.292    175.98127            0    3681.5299   -16.345167 
     950    20968.166    186.59847            0    3681.2929    -2.330456 
    1000     20490.66    266.19375            0    3681.3037    11.787983 
    1050    20222.396    310.94072            0      3681.34   -8.3459539 
    1100    21321.687    127.61533            0    3681.2299   -1.2184718 
    1150    20849.582    206.01695            0    3680.9472   -0.8669916 
    1200    21815.003    45.317417            0    3681.1512    1.5988314 
    1250    18655.437    572.41453            0     3681.654    10.064076 
    1300    20780.781    217.36504            0    3680.8286    6.0538619 
    1350    20558.972     254.3648            0    3680.8601   -3.6773987 
    1400    21485.029    99.812949            0    3680.6511   -16.185471 
    1450    21771.108     52.15959            0    3680.6775   -2.4756681 
    1500    21520.948    93.503949            0    3680.3286    2.1023578 
    1550    21351.418     121.6814            0    3680.2511    5.5159978 
    1600    20778.805    216.92171            0    3680.0559    15.089182 
    1650    21477.639     100.2182            0    3679.8247   -1.1045944 
    1700    18501.343    596.47853            0    3680.0357    -15.67963 
    1750    18563.643    587.34767            0    3681.2882    33.532167 
    1800     19110.19    494.82264            0    3679.8543    18.024034 
    1850    21364.196    119.23454            0    3679.9339    2.5291491 
    1900    20146.643    322.14595            0    3679.9197     5.731152 
    1950     20692.67    231.25357            0    3680.0319    4.2977641 
    2000    20943.904    189.11223            0     3679.763   -22.645645 
    2050    19668.152    401.81407            0    3679.8394    3.6255896 
    2100    20280.572    299.73976            0    3679.8351    7.4809355 
    2150    19182.121    483.47905            0    3680.4992    22.615309 
    2200     21299.76    130.77281            0    3680.7327    4.7114154 
    2250    20487.784     266.4995            0    3681.1302   -8.6406776 
    2300    18655.125    571.91487            0    3681.1023   -5.2671669 
    2350    21512.614    95.766913            0    3681.2025   -9.3523428 
    2400    21467.773    103.31519            0    3681.2773   -29.600307 
    2450    20096.937    332.80159            0    3682.2911    35.890912 
    2500    20761.446    222.16118            0    3682.4022   -12.528127 
    2550      20409.6    280.67234            0    3682.2723   -22.277373 
    2600    21469.964    103.95529            0    3682.2826   -10.038267 
    2650    20708.138    231.00516            0    3682.3615    5.3659502 
    2700    18584.743    585.07862            0    3682.5357    21.785261 
    2750    20503.019    264.91491            0    3682.0847   -4.5583917 
    2800    20584.075    251.44664            0    3682.1258   -6.5084595 
    2850    17277.076    802.33356            0    3681.8462    15.519513 
    2900    19392.956    449.92915            0    3682.0885   -4.3829957 
    2950    18371.786    620.29835            0    3682.2626    7.2117592 
    3000    20412.015    280.25302            0    3682.2555   0.32492606 
    3050    20858.248    205.65269            0    3682.0273    4.5055715 
    3100    21561.094    88.438447            0    3681.9541   -3.7523733 
    3150    15471.278    1103.4497            0    3681.9961   -14.576367 
    3200    15386.973    1117.8815            0     3682.377    15.051163 
    3250    19741.037    392.04755            0    3682.2204   -2.6610995 
    3300    20870.191    203.58229            0    3681.9475   -4.7795545 
    3350    16648.228    907.66571            0    3682.3704   -8.9242511 
    3400    20104.016    331.58603            0    3682.2554    6.4783858 
    3450    21421.316    112.28228            0    3682.5015   -8.3484987 
    3500    19284.533    467.80739            0    3681.8962   -12.835452 
    3550    20160.125     322.4476            0    3682.4684    1.6574827 
    3600    16682.415    902.73752            0      3683.14    22.383296 
    3650     16762.19    890.14636            0    3683.8446    16.119412 
    3700    17858.568    707.37212            0       3683.8   -1.6582504 
    3750    20029.881    345.15986            0    3683.4733   -3.1415889 
    3800        20734    227.99158            0    3683.6582   -7.9580418 
    3850    20741.089    226.39408            0    3683.2423    8.3055765 
    3900    18671.251    571.42296            0    3683.2981   -3.7468858 
    3950    19547.209    423.14256            0    3681.0108    5.8312279 
    4000    19739.799    393.58799            0    3683.5544    18.604884 
    4050    20014.121     347.8176            0    3683.5044      9.93387 
    4100    20503.654    266.08691            0    3683.3626    8.1304118 
    4150    18309.702    632.29807            0    3683.9151 -0.0021480359 
    4200    20509.423    265.60353            0    3683.8408   -2.1658857 
    4250    21805.541    50.325935            0    3684.5828     1.082842 
    4300    21420.551    114.90431            0    3684.9962   -1.7985998 
    4350    20256.928    308.74187            0    3684.8966   -11.669472 
    4400    21633.488    79.629274            0    3685.2106  -0.96131785 
    4450    20793.327    219.66955            0    3685.2241    1.3752349 
    4500    18719.484    564.86754            0    3684.7816    2.6308699 
    4550    20966.335    190.68308            0    3685.0722   -18.587627 
    4600    19428.962    446.59618            0    3684.7565   -4.4051672 
    4650    18408.956    616.85009            0    3685.0095     2.777272 
    4700    19215.779    482.57562            0    3685.2054    19.441016 
    4750    20155.927    326.13401            0    3685.4553    6.1734993 
    4800    20918.085    199.31832            0    3685.6659    3.4407437 
    4850    20236.958    312.07276            0     3684.899    3.2612893 
    4900     21419.89    115.36879            0    3685.3505    -4.675951 
    4950    19707.901    401.14828            0    3685.7985   -10.730734 
    5000    19407.201    450.64394            0    3685.1775    17.518981 
    5050    21527.598    97.655186            0    3685.5882   -9.2294707 
    5100    21581.933    88.595517            0    3685.5843   -20.669485 
    5150    21161.214    158.48503            0    3685.3541   -2.7587502 
    5200    21166.679    157.24762            0    3685.0275   -18.180044 
    5250    20909.576    200.23507            0    3685.1644   -16.617303 
    5300    21911.746    33.236563            0    3685.1942   -5.8313967 
    5350    20857.303    208.87453            0    3685.0916    12.176312 
    5400     20958.96    191.96694            0    3685.1269    3.6116429 
    5450    20433.179    279.61178            0    3685.1415    13.324529 
    5500    19604.675    416.88499            0    3684.3308    21.536484 
    5550    18171.145    655.92915            0    3684.4534   -9.2269804 
    5600    19799.907    385.12116            0    3685.1056    22.202165 
    5650    19711.882    399.30581            0    3684.6194     15.93063 
    5700    17908.833    699.52405            0    3684.3295   0.35530356 
    5750    18606.518      583.538            0    3684.6243   -4.4540843 
    5800    21814.053    48.974627            0    3684.6501   -1.5206358 
    5850    18029.107     679.9357            0    3684.7868    12.137677 
    5900    21090.739    169.64502            0    3684.7682   -1.5051545 
    5950     21086.26    170.29075            0    3684.6674   -2.8164474 
    6000    21285.771    136.95608            0    3684.5846   -26.582739 
    6050    21203.994    150.87822            0    3684.8772   -2.6617226 
    6100    21481.553    104.57796            0    3684.8368   -16.524974 
    6150      20354.4    292.57675            0    3684.9767    2.7960207 
    6200    21326.591    130.75243            0    3685.1843   -1.5929194 
    6250    21505.087    101.07817            0    3685.2593   -3.7821931 
    6300    21296.273     135.6593            0    3685.0382  -0.55635908 
    6350    21295.389    135.86485            0    3685.0964    5.6614093 
    6400    16552.242    926.02655            0    3684.7336    14.177218 
    6450    20148.951     327.1151            0    3685.2736    7.4561085 
    6500    20962.151    191.79415            0     3685.486   -4.5436711 
    6550    21710.328    67.433972            0    3685.8219   -5.7678572 
    6600    20698.571    234.79099            0    3684.5528   -2.1984068 
    6650    17892.287    704.05484            0    3686.1026    11.525836 
    6700    21272.999    141.26589            0    3686.7657   0.44088069 
    6750    19558.993    426.46448            0    3686.2966   -16.907401 
    6800    20350.247    295.23951            0    3686.9474    1.1284348 
    6850     18665.05     573.5326            0    3684.3742    17.088712 
    6900    19769.199     392.1551            0    3687.0216    6.7562425 
    6950    19439.159    446.99138            0    3686.8512   -6.0105763 
    7000    19379.907    456.53471            0    3686.5192   -9.0505095 
    7050    19983.754    356.02523            0     3686.651   -5.6274314 
    7100    19867.737    375.47627            0    3686.7658    17.315482 
    7150    19258.794    477.47344            0    3687.2724    14.316676 
    7200    21282.428    139.96051            0    3687.0318  -0.77043459 
    7250    19828.603    381.98919            0    3686.7564    6.5142869 
    7300    20574.582     257.8245            0    3686.9215   -3.6547118 
    7350    21613.467    84.771568            0    3687.0161   -7.5188826 
    7400    21817.009    50.844944            0    3687.0131   -14.888864 
    7450    14937.538    1197.4257            0    3687.0154    1.7540499 
    7500    18326.914    632.40374            0    3686.8894    8.3397357 
    7550    13611.007    1418.4727            0    3686.9739   -19.379482 
    7600    19173.985     491.9482            0    3687.6123    17.229001 
    7650    16911.504    867.33649            0    3685.9204   -21.042834 
    7700    21752.116    61.143705            0    3686.4963   -10.344487 
    7750    20208.337    318.26355            0    3686.3197    13.385814 
    7800    21649.909    77.950987            0    3686.2692   -1.7911084 
    7850     20139.64    329.50319            0    3686.1098   -5.5805093 
    7900    21355.026     126.7642            0    3685.9352   -7.7062172 
    7950    21336.178    129.88925            0    3685.9188    -2.059298 
    8000    21047.596    177.71546            0    3685.6482   0.37963466 
    8050    19217.351    482.62331            0    3685.5152    6.5582595 
    8100    20499.057     268.7173            0    3685.2268   -1.1959737 
    8150    21494.301    102.83829            0    3685.2219   -1.6427647 
    8200    20074.928    339.19817            0    3685.0195     6.285123 
    8250    17335.157    793.47566            0    3682.6685    22.877381 
    8300    17340.544    794.62619            0    3684.7168    3.9147755 
    8350    20529.345    262.51162            0    3684.0691     4.031768 
    8400    18884.747    537.47827            0    3684.9361    22.853404 
    8450     20341.86    293.10484            0    3683.4148   0.33856656 
    8500    19300.282    467.58127            0    3684.2949     12.35507 
    8550    21631.936    78.254534            0    3683.5772   -10.992959 
    8600    20204.913    316.83233            0    3684.3178     20.74228 
    8650    21018.189    181.32054            0     3684.352    1.8412068 
    8700    20161.304    323.97907            0    3684.1964    -2.646629 
    8750     19081.79    504.00155            0    3684.2998   -10.088053 
    8800    20834.489    211.76247            0    3684.1773    14.896336 
    8850    20929.355    196.18335            0    3684.4092   -1.2602398 
    8900    21491.074    102.47788            0    3684.3235   -1.4696758 
    8950    20474.735    271.69461            0    3684.1504   -6.9489258 
    9000    21128.641    162.40732            0    3683.8474   -7.7928168 
    9050    18421.801    614.46442            0    3684.7646     24.40313 
    9100    19301.292    466.98873            0    3683.8707    4.4687046 
    9150    21575.705    88.213763            0    3684.1646  -0.94696984 
    9200    20004.776    350.05448            0    3684.1838   -7.3466605 
    9250    21384.079    120.14472            0    3684.1578   -8.3773844 
    9300    21980.599    20.702393            0    3684.1356   -12.666293 
    9350    21686.606    69.517984            0    3683.9524   -8.8366533 
    9400    20732.704    228.46247            0    3683.9131   -6.4080307 
    9450    19798.859    384.34696            0    3684.1568    7.6198484 
    9500    20270.695    305.22664            0    3683.6758    1.5862486 
    9550    16496.156    935.28481            0    3684.6441    15.001468 
    9600    20642.429    241.08853            0    3681.4934   -9.2159382 
    9650    21292.587     135.4474            0    3684.2119  -0.54770976 
    9700    18888.158    536.60518            0    3684.6315    5.3236926 
    9750    18750.018    559.35922            0    3684.3623   -9.9424949 
    9800    20544.772    259.71076            0    3683.8394     8.732202 
    9850    16698.125    901.90076            0    3684.9216    9.9553329 
    9900    21450.963    109.58687            0    3684.7474   -4.8001999 
    9950    20664.461    240.66995            0    3684.7468   -3.4840781 
   10000    18951.367    526.45428            0    3685.0155    21.512727 
Loop time of 8.99246 on 4 procs for 10000 steps with 81 atoms

Performance: 9608.051 tau/day, 1112.043 timesteps/s
93.8% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.01308    | 0.038162   | 0.084123   |  14.4 |  0.42
Neigh   | 0.017227   | 0.032774   | 0.061983   |  10.0 |  0.36
Comm    | 1.329      | 1.5822     | 1.8017     |  13.5 | 17.60
Output  | 0.014984   | 0.029676   | 0.046035   |   6.6 |  0.33
Modify  | 6.8022     | 7.1104     | 7.4356     |   8.6 | 79.07
Other   |            | 0.1992     |            |       |  2.22

Nlocal:    20.25 ave 81 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost:    46.25 ave 95 max 14 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs:    249.25 ave 997 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1

Total # of neighbors = 997
Ave neighs/atom = 12.3086
Neighbor list builds = 993
Dangerous builds = 943

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:00:09
